Epistasis decreases with increasing antibiotic pressure

Data and code for 'Epistasis decreases with increasing antibiotic pressure but not temperature'

All of the competition data and code used to run the analysis presented in the manuscript "Epistasis decreases with increasing antibiotic pressure but not temperature" is available here. The bioRxiv pre-print is found here: https://doi.org/10.1101/2022.09.01.506172. The publication will appear in Philosophical Transactions of the Royal Society B: Biological Sciences on 03 April 2023 at the following permanent link: https://dx.doi.org/10.1098/rstb.2022.0058.

All flow cytometry and estimated competitive fitness data is found in the 'data' folder. The data files include raw data files as well as intermediate data files that were created along the course of the analysis. Running the `.Rmd` files locally may over-write these intermediate data files (if you're trying to re-create these intermediate data files but it's not working, remember to check whether `eval=FALSE` in the header of the chunk).

Analyses are found in the 'analysis' folder. For R notebook files, the code is available in the `.Rmd` files and is best run using RStudio (but the `.Rmd` files can also be opened for viewing with any text editor). Intermediate data files in the 'analysis' folder have the extension `.RData` or `.dat`; running R and python files locally may over-write these intermediate data files. The output of each R notebook file has also been saved to `.html` files. It is therefore easiest to start by viewing the `.html` file for each R notebook and then opening `.Rmd` files only if you wish to alter the code.

The python code calculates gamma epistasis and parametric bootstrapping of the gamma epistasis values.